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Using this numbered version of the image (which is huge, and I couldn't find an easy way to scale down in the post) as a reference, here's the complete list (some answers from the older games taken from here):

Three figures that are extremely blurry. Given their positioning and the number of them, I'd guess they're meant to be the three Goddesses (mentioned in legends in pretty much all the games): Nayru, Farore and Din

Kaepora Gaebora from Ocarina of Time (and other games)

Rauru from Ocarina of Time

Impa from Ocarina of Time

Saria from Ocarina of Time

Supposedly the King of Hyrule, though not sure from which game

Nabooru from Ocarina of Time

Princess Ruto (adult) from Ocarina of Time

Darunia from Ocarina of Time

Link from all games, though most closely resembles the one from Twilight Princess

Princess Zelda from all games, though again seems to most closely resemble the one from Twilight Princess

Ganondorf

Wind Fish

Great Fairy from Wind WakerUnnumbered Fairy next to the Great Fairy: possibly Ciela from Phantom Hourglass

Great Fairy from Twilight Princess

Great Fairy from Majora's Mask (also from Ocarina of Time, since they shared character models, but she's holding the Great Fairy Sword that is specific to Majora's Mask)

Valoo from Wind Waker

Fi from Skyward Sword

Presumably Navi from Ocarina of Time

Tatl (Link's companion fairy) from Majora's Mask

Tael from Majora's Mask

The Great Deku Tree from Ocarina of Time

Fado from Wind Waker

Deku Tree Sprout from Ocarina of Time

Makar from Wind Waker

Fairy Queen from Wind Waker

Medli from Wind Waker

Laruto from Wind Waker

Lord Jabu-Jabu from Ocarina of Time

Renado from Twilight Princess

Rusl from Twilight Princess

Ashei from Twilight Princess

Shad from Twilight Princess

Auru from Twilight Princess

Tarin from Link's Awakening

Marin from Link's Awakening

Ilia from Twilight Princess

Epona from most games, though appears to most closely resemble Epona from Twilight Princess

Talon from Ocarina of Time

Ingo from Ocarina of Time

Anju from Majora's Mask

Kafei from Majora's Mask

Linebeck from Phantom Hourglass

Tetra from Wind Waker

Gonzo from Wind Waker

Senza from Wind Waker

Nudge from Wind Waker

Tijo from Majora's Mask

Tingle from Majora's Mask (and other games)

Cremia from Majora's Mask

Niko from Wind Waker

Zuko from Wind Waker

(Link's) Grandmother from Wind Waker

Evan from Majora's Mask

Toto from Majora's Mask

Lulu from Majora's Mask

Romani from Majora's Mask

Ralph from Oracle of Ages

Mako from Wind Waker

Maple from Oracle of Ages

Darmani III from Majora's Mask

Japas from Majora's Mask

Mikau from Majora's Mask

Skull Kid from Majora's Mask

Mido from Ocarina of Time

Goron Elder from Majora's Mask

Goron Elder's son from Majora's Mask

Deku King from Majora's Mask

Deku Princess from Majora's Mask (with Link in Deku form?)

Deku Butler from Majora's Mask

King of Red Lions from Wind Waker

Byrne from Spirit Tracks

Anjean from Spirit Tracks

Midna from Twilight Princess

Oshus from Phantom Hourglass

Sahasrahla from A Link to the Past

Ezlo from The Minish Cap

Travelling Mask Salesman from Majora's Mask

Bellum from Phantom Hourglass

Veran from Oracle of Ages

Zant from Twilight Princess

Agahnim from A Link to the Past

Vaati from The Minish Cap

Onox from Oracle of Seasons

One of the four giants from Majora's Mask

Koume from Majora's Mask (also appears as the boss of the Spirit Temple in Ocarina of Time)

The Moon from Majora's Mask

Kotake from Majora's Mask (also appears as the boss of the Spirit Temple in Ocarina of Time)

@Valorum That video is painful to watch which is why I didn't use it originally, but it's not quite so bad once I could skip through the video to the answers I still needed or wanted to confirm.
– Anthony GristSep 4 '16 at 18:00

It contains all the answers, which is good enough for me
– ValorumSep 4 '16 at 18:34

Sorry it took so long to get back to this. I made some edits according to my own knowledge. It looks good to me now.
– RelixSep 9 '16 at 18:08